📝 Document FCP-INDI/C-PAC#2152 + FCP-INDI/C-PAC#2153

[shnizzedy]

Documents

Documents FCP-INDI/C-PAC#2152 by Shinwon Park
Documents FCP-INDI/C-PAC#2153 by @shnizzedy

Description

Adds

• documentation regarding this bug and its resolution to Troubleshooting and Help § Recently Resolved Common Issues
• warnings linking to that documentation in places where bandpass filtering is mentioned in the user docs:
  • Nuisance Signal Regression
    • § Configuring Nuisance Signal Regression Options: Configuring Temporal Filtering Options: 2. Select regressors
    • § Pulling Regressors from fMRIPrep Output Directory
  • Pre-configured Pipelines § human: default: The Default Pipeline
    • After

      The default processing pipeline performs fMRI processing using four strategies, with and without global signal regression, with and without bandpass filtering.

    • After

      The residuals of the NVR procedure are processed with and without bandpass filtering (0.01Hz < f < 0.1Hz), written into MNI space at 3mm resolution and subsequently smoothed using a 6mm FWHM kernel.

    • After

      Amplitude of low frequency fluctuations (alff)^[9]: the variance of each voxel is calculated after bandpass filtering in original space and subsequently written into MNI space at 2mm resolution and spatially smoothed using a 6mm FWHM kernel.

    • After

      Fractional amplitude of low frequency fluctuations (falff)^[10]: Similar to alff except that the variance of the bandpassed signal is divided by the total variance (variance of non-bandpassed signal).

  • C-PAC Quickstart § Default Pipeline
    • Same places as in Pre-configured Pipelines § human: default: The Default Pipeline

SSOTs default pipeline description (same text, slightly out of sync, was present in Pre-configured Pipelines § human: default: The Default Pipeline and C-PAC Quickstart § Default Pipeline)

Screenshots

Troubleshooting and Help § Recently Resolved Common Issues

Nuisance Signal Regression

Pre-configured Pipelines § human: default: The Default Pipeline

C-PAC Quickstart § Default Pipeline

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the source branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I tried letting the CI build this branch on a fork or built the project locally and verified that there are no visible errors.

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